Regulation Of Transcriptional Activity Research Articles

DYRK1A is a multifunctional host factor that regulates coronavirus replication in a kinase-independent manner.

Coronaviruses (CoVs) pose a major threat to human and animal health worldwide, which complete viral replication by hijacking host factors. Identifying host factors essential for the viral life cycle can deepen our understanding of the mechanisms of virus-host interactions. Based on our previous genome-wide CRISPR screen of α-CoV transmissible gastroenteritis virus (TGEV), we identified the host factor dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A), but not DYRK1B, as a critical factor in TGEV replication. Rescue assays and kinase inhibitor experiments revealed that the effect of DYRK1A on viral replication is independent of its kinase activity. Nuclear localization signal modification experiments showed that nuclear DYRK1A facilitated virus replication. Furthermore, DYRK1A knockout significantly downregulated the expression of the TGEV receptor aminopeptidase N (ANPEP) and inhibited viral entry. Notably, we also demonstrated that DYRK1A is essential for the early stage of TGEV replication. Transmission electron microscopy results indicated that DYRK1A contributes to the formation of double-membrane vesicles in a kinase-independent manner. Finally, we validated that DYRK1A is also a proviral factor for mouse hepatitis virus, porcine deltacoronavirus, and porcine sapelovirus. In conclusion, our work demonstrated that DYRK1A is an essential host factor for the replication of multiple viruses, providing new insights into the mechanism of virus-host interactions and facilitating the development of new broad-spectrum antiviral drugs.IMPORTANCECoronaviruses, like other positive-sense RNA viruses, can remodel the host membrane to form double-membrane vesicles (DMVs) as their replication organelles. Currently, host factors involved in DMV formation are not well defined. In this study, we used transmissible gastroenteritis virus (TGEV) as a virus model to investigate the regulatory mechanism of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) on coronavirus. Results showed that DYRK1A significantly inhibited TGEV replication in a kinase-independent manner. DYRK1A knockout (KO) can regulate the expression of receptor aminopeptidase N (ANPEP) and endocytic-related genes to inhibit virus entry. More importantly, our results revealed that DYRK1A KO notably inhibited the formation of DMV to regulate the virus replication. Further data proved that DYRK1A is also essential in the replication of mouse hepatitis virus, porcine deltacoronavirus, and porcine sapelovirus. Taken together, our findings demonstrated that DYRK1A is a conserved factor for positive-sense RNA viruses and provided new insights into its transcriptional regulation activity, revealing its potential as a candidate target for therapeutic design.

Emerging role of YAP/TAZ in vascular mechanotransduction and disease.

Cells have an incredible ability to physically interact with neighboring cells and their environment. They can detect and respond to mechanical forces by converting mechanical stimuli into biochemical signals in a process known as mechanotransduction. This is a key process for the adaption of vascular smooth muscle and endothelial cells to altered flow and pressure conditions. Mechanical stimuli, referring to a physical force exerted on cells, are primarily sensed by transmembrane proteins and the actin cytoskeleton, which initiate a cascade of intracellular events, including the activation of signaling pathways, ion channels, and transcriptional regulators. Recent work has highlighted an important role of the transcriptional coactivators YAP/TAZ for mechanotransduction in vascular cells. Interestingly, the activity of YAP/TAZ decreases with age, providing a potential mechanism for the detrimental effects of aging in the vascular wall. In this review, we summarize the current knowledge on the functional role of YAP and TAZ in vascular endothelial and smooth muscle cells for mechanotransduction in homeostasis and disease. In particular, the review is focused on invivo observations from conditional knockout (KO) models of YAP/TAZ and the potential implications these studies may have for our understanding of vascular disease development.

Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter

Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacked on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reactivation or viral latency.

PSI-10 Prioritizing Fertility-Related Genes in Cattle Through Systems Genomics Data Integration

Abstract Female fertility significantly affects the efficiency of cow-calf production. Despite the collective efforts to understand the complex regulation of reproductive traits, causative genes and/or mutations have yet to be reported. Using omics technologies, such as gene expression, may unveil potential regulatory mechanisms and provide opportunities that link genotype to phenotype. Among them, expression quantitative trait loci (eQTL) are a powerful tool to identify biological mechanisms and potential markers for improving fertility. This study aimed to identify eQTLs underlying fertility-related traits and their co-localization with previously annotated QTLs. RNA-Seq from uterine epithelial cells (GSE171577) from crossbreed cows (n = 18 non-pregnant – NP and n = 25 pregnant – P) were used for gene expression analysis and SNP calling. Raw data quality control was performed, and read mapping was carried out using STAR. Genes were normalized to counts per million (CPM) and then the CPM values were log2 transformed using edgeR. Next, uniquely mapped reads were used for variant detection using the GATK software. Significant eQTLs were compared with the Animal Genome cattle database (QTLdb) to identify overlapping QTL regions. After quality control, 43 samples, 203,404 SNPs, and 15,029 genes were used for eQTL analysis. Using an additive linear model from the Matrix eQTL R-package, we identified 3,989 cis- and 7,683 trans-eQTLs for 1,120 and 2,503 genes, respectively (FDR < 0.05). A total of 50 cis-eQTLs were previously reported as differentially expressed genes, including CD37, CXCL3, PILRA, and PPP6R1 genes. The QTLs from QTLdb overlapping with our eQTLs were associated with traits such as age at puberty, conception rate, fertility index, and luteal activity (FDR < 0.05). Additionally, QTLs for production traits, such as milk production and body weight gain, were over-represented by the eQTLs we have identified. Significant biological processes underlying cis-regulated genes retrieved from ShinyGO were related to antigen processing and presentation. Likewise, trans-eQTLs genes were involved with transcription cis-regulatory region binding and transcription regulator activity. Our study provides novel regulatory and potential causative genetic variants, biological pathways, and genes underlying fertility in cows. Annotation and co-localization of detected eQTLs retrieved genomic regions previously reported as QTLs for production and reproduction-related traits. Further investigation, however, is required to untangle the mechanisms modulating gene expression and its effects on fertility-related traits.

PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer.

The promyelocytic leukemia (PML) protein organizes nuclear aggregates known as PML nuclear bodies (PML-NBs), where many transcription factors localize to be regulated. In addition, associations of PML and PML-NBs with chromatin are described in various cell types, further implicating PML in transcriptional regulation. However, a complete understanding of the functional consequences of PML association to DNA in cellular contexts where it promotes relevant phenotypes is still lacking. We examined PML chromatin association in triple-negative breast cancer (TNBC) cell lines, where it exerts important oncogenic functions. We find that PML associates discontinuously with large heterochromatic PML-associated domains (PADs) that contain discrete gene-rich euchromatic sub-domains locally depleted of PML. PML promotes heterochromatic organization in PADs and expression of pro-metastatic genes embedded in these sub-domains. Importantly, this occurs outside PML-NBs, suggesting that nucleoplasmic PML exerts a relevant gene regulatory function. We also find that PML plays indirect regulatory roles in TNBC cells by promoting the expression of pro-metastatic genes outside PADs. Our findings suggest that PML is an important transcriptional regulator of pro-oncogenic metagenes in TNBC cells, via transcriptional regulation and epigenetic organization of heterochromatin domains that embed regions of local transcriptional activity.

CUT homeobox genes: transcriptional regulation of neuronal specification and beyond.

CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.

Single-cell RNA sequencing of murine hearts for studying the development of the cardiac conduction system

The development of the cardiac conduction system (CCS) is essential for correct heart function. However, critical details on the cell types populating the CCS in the mammalian heart during the development remain to be resolved. Using single-cell RNA sequencing, we generated a large dataset of transcriptomes of ~0.5 million individual cells isolated from murine hearts at six successive developmental corresponding to the early, middle and late stages of heart development. The dataset provides a powerful library for studying the development of the heart’s CCS and other cardiac components. Our initial analysis identified distinct cell types between 20 to 26 cell types across different stages, of which ten are involved in forming the CCS. Our dataset allows researchers to reuse the datasets for data mining and a wide range of analyses. Collectively, our data add valuable transcriptomic resources for further study of cardiac development, such as gene expression, transcriptional regulation and functional gene activity in developing hearts, particularly the CCS.

In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation.

In organisms that use reduced sulfur compounds as alternative or additional electron donors to organic compounds, transcriptional regulation of genes for enzymes involved in sulfur oxidation is needed to adjust metabolic flux to environmental conditions. However, little is known about the sensing and response to inorganic sulfur compounds such as thiosulfate in sulfur-oxidizing bacteria. In the Alphaproteobacterium Hyphomicrobium denitrificans, one strategy is the use of the ArsR-SmtB-type transcriptional regulator SoxR. We show that this homodimeric repressor senses sulfane sulfur and that it is crucial for the expression not only of sox genes encoding the components of a truncated periplasmic thiosulfate-oxidizing enzyme system but also of several other sets of genes for enzymes of sulfur oxidation. DNA binding and transcriptional regulatory activity of SoxR are controlled by polysulfide-dependent cysteine modification. The repressor uses the formation of a sulfur bridge between two conserved cysteines as a trigger to bind and release DNA and can also form a vicinal disulfide bond to orchestrate a response to oxidizing conditions. The importance of the sulfur bridge forming cysteines was confirmed by site-directed mutagenesis, mass spectrometry, and gel shift assays. In vivo, SoxR interacts directly or indirectly with a second closely related repressor, sHdrR.

SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways.

Despite extensive studies on the effects of SARS-CoV-2 infection, there is still a lack of understanding of the downstream epigenetic and regulatory alterations in infected cells. In this study, we investigated changes in enhancer acetylation in epithelial lung cells infected with SARS-CoV-2 and their influence on transcriptional regulation and pathway activity. To achieve this, we integrated and reanalyzed data of enhancer acetylation, ex-vivo infection and single cell RNA-seq data from human patients. Our findings revealed coordinated changes in enhancers and transcriptional networks. We found that infected cells lose the WT1 transcription factor and demonstrate disruption of WT1-bound enhancers and of their associated target genes. Downstream targets of WT1 are involved in the regulation of the Wnt signaling and the mitogen-activated protein kinase cascade, which indeed exhibit increased activation levels. These findings may provide a potential explanation for the development of pulmonary fibrosis, a lethal complication of COVID-19. Moreover, we revealed over-acetylated enhancers associated with upregulated genes involved in cell adhesion, which could contribute to cell-cell infection of SARS-CoV-2. Furthermore, we demonstrated that enhancers may play a role in the activation of pro-inflammatory cytokines and contribute to excessive inflammation in the lungs, a typical complication of COVID-19. Overall, our analysis provided novel insights into the cell-autonomous dysregulation of enhancer regulation caused by SARS-CoV-2 infection, a step on the path to a deeper molecular understanding of the disease.

The 14-3-3 protein OsGF14f interacts with OsbZIP23 and enhances its activity to confer osmotic stress tolerance in rice.

Drought, which can induce osmotic stress, is the leading environmental constraint to crop productivity. Plants in both agricultural and natural settings have developed various mechanisms to cope with drought stress. The identification of genes associated with drought stress tolerance and understanding the underlying regulatory mechanisms are prerequisites for developing molecular manipulation strategies to address this issue. Here, we reported that the 14-3-3 protein OsGF14f (G-BOX FACTOR 14-3-3f), positively modulates osmotic stress tolerance in rice (Oryza sativa). OsGF14f transgenic lines had no obvious change in crucial agronomic traits including yield and plant height. OsGF14f is transcriptionally induced by PEG treatment, and in rice, overexpression or knockout of this gene leads to enhanced or weakened osmotic stress tolerance, respectively. Furthermore, OsGF14f positively regulates abscisic acid (ABA) responses by interacting with the core ABA-responsive transcription factor OsbZIP23 (BASIC LEUCINE ZIPPER 23) to enhance its transcriptional regulation activity toward downstream target genes. Further genetic analysis showed that OsGF14f is required for the full function of OsbZIP23 in rice osmotic response and OsGF14f-mediated osmotic stress tolerance partially depends on OsbZIP23. Interestingly, OsGF14f is a direct target gene of OsbZIP23. Taken together, our findings reveal a genetic and molecular framework by which the OsGF14f-OsbZIP23 complex modulates rice osmotic response, providing targets for developing drought-tolerant crops.

#5865 BET INHIBITION DIMINISHES CELLULAR SENESCENCE IN CULTURED TUBULAR EPITHELIAL CELLS

Abstract Background and Aims Chronic kidney disease (CKD) can be considered an age-related disorder. Recent studies have shown the involvement of the activation of cellular senescence mechanisms in the kidney and aging. Intensive research to develop pharmacological approaches targeting cellular senescence is under investigation. Among novel therapeutic options, epigenetic drugs, such as bromodomain and extra terminal BET inhibitors, are being widely explored in proliferative, immune and chronic inflammatory diseases, including CKD. These drugs regulate transcription activation of cell cycle control and proinflammatory factors. There are not studies about the potential effect of BET inhibitors on cellular senescence in the kidney despite the fact that tubular epithelial cells are frequently implicated in kidney senescence. Method To study this, we evaluate the effect of JQ1, a BET inhibitor, on cellular senescence in primary cell culture of murine tubular epithelial cells (TECs) using Adriamycin as a senescence inducer verified by B-galactosidase assay. Next, we evaluated the effect of JQ1 on gene expression levels of cell cycle markers, components of senescence-associated secretory phenotype (SASP) as well as anti-apoptotic and antioxidant markers, all of them related to senescence program. Results Our results indicated that JQ1 significantly decreased Adriamycin-induced p21 gene upregulation, a primordial cell cycle arrest factor. This BET inhibitor also downregulated SAPS genes, such as Tgfb1, Il1b, Ctgf, Ccl2 and Il6 overexpression in Adriamycin-treated tubular cells. Likewise, anti-apoptotic Bcl-xl and antioxidant factors Cat, Hmox-1, Nox-4 and Nrf2 mRNA levels were significantly restored by JQ1. Conclusion In conclusion, the present study highlights the use of JQ1 as a therapeutic option to ameliorate tubular cellular senescence-associated markers. These data support the potential use of BET inhibitors in chronic kidney diseases.

Research Note: Identification of core promoter region of the polyunsaturated fatty acid synthesis-related gene family in chicken

Chicken is considered an ideal model species to study the synthesis of polyunsaturated fatty acids (PUFAs) due to its appropriate proportions of fatty acids and abundant content of PUFAs, suitable for human consumption. However, the molecular mechanisms regulating poultry PUFA synthesis remain unclear. Here, we systematically explored the transcriptional regulation activity of the gene family related to PUFA synthesis in chicken by carrying out the Dual-Luciferase Reporter Assay. We identified the core promoter regions of members of the chicken PUFA synthesis-related gene family, including ELOVL1, ELOVL2, ELOVL3, ELOVL4, ELOVL5, ELOVL6, ELOVL7, FADS1, FADS2, FADS6, SCD, and SCD5. Additionally, changes in relative fluorescence values of different truncated segments in the upstream regulatory region of these genes indicate the existence of regulatory regions. Furthermore, we predicted the transcription factors that bind to the identified core promoter regions of multiple genes, including Sp1, NF-1, C/EBPalpha, etc. These findings provide a basis for the molecular mechanisms regulating poultry PUFA synthesis and offer new scientific insight into the potential improvement of poultry meat quality in the future.

Allelic variation in transcription factor PtoWRKY68 contributes to drought tolerance in Populus.

Drought stress limits woody species productivity and influences tree distribution. However, dissecting the molecular mechanisms that underpin drought responses in forest trees can be challenging due to trait complexity. Here, using a panel of 300 Chinese white poplar (Populus tomentosa) accessions collected from different geographical climatic regions in China, we performed a genome-wide association study (GWAS) on seven drought-related traits and identified PtoWRKY68 as a candidate gene involved in the response to drought stress. A 12-bp insertion and/or deletion and three nonsynonymous variants in the PtoWRKY68 coding sequence categorized natural populations of P. tomentosa into two haplotype groups, PtoWRKY68hap1 and PtoWRKY68hap2. The allelic variation in these two PtoWRKY68 haplotypes conferred differential transcriptional regulatory activities and binding to the promoters of downstream abscisic acid (ABA) efflux and signaling genes. Overexpression of PtoWRKY68hap1 and PtoWRKY68hap2 in Arabidopsis (Arabidopsis thaliana) ameliorated the drought tolerance of two transgenic lines and increased ABA content by 42.7% and 14.3% compared to wild-type plants, respectively. Notably, PtoWRKY68hap1 (associated with drought tolerance) is ubiquitous in accessions in water-deficient environments, whereas the drought-sensitive allele PtoWRKY68hap2 is widely distributed in well-watered regions, consistent with the trends in local precipitation, suggesting that these alleles correspond to geographical adaptation in Populus. Moreover, quantitative trait loci analysis and an electrophoretic mobility shift assay showed that SHORT VEGETATIVE PHASE (PtoSVP.3) positively regulates the expression of PtoWRKY68 under drought stress. We propose a drought tolerance regulatory module in which PtoWRKY68 modulates ABA signaling and accumulation, providing insight into the genetic basis of drought tolerance in trees. Our findings will facilitate molecular breeding to improve the drought tolerance of forest trees.

Bifunctional protein ArsRM contributes to arsenite methylation and resistance in Brevundimonas sp. M20

BackgroundArsenic (As) with various chemical forms, including inorganic arsenic and organic arsenic, is the most prevalent water and environmental toxin. This metalloid occurs worldwide and many of its forms, especially arsenite [As(III)], cause various diseases including cancer. Organification of arsenite is an effective way for organisms to cope with arsenic toxicity. Microbial communities are vital contributors to the global arsenic biocycle and represent a promising way to reduce arsenite toxicity.MethodsBrevundimonas sp. M20 with arsenite and roxarsone resistance was isolated from aquaculture sewage. The arsHRNBC cluster and the metRFHH operon of M20 were identified by sequencing. The gene encoding ArsR/methyltransferase fusion protein, arsRM, was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25–6 mM As(III), aresenate, or pentavalent roxarsone. The methylation activity and regulatory action of ArsRM were analyzed using Discovery Studio 2.0, and its functions were confirmed by methyltransferase activity analysis and electrophoretic mobility shift assays.ResultsThe minimum inhibitory concentration of the roxarsone resistant strain Brevundimonas sp. M20 to arsenite was 4.5 mM. A 3,011-bp arsenite resistance ars cluster arsHRNBC and a 5649-bp methionine biosynthesis met operon were found on the 3.315-Mb chromosome. Functional prediction analyses suggested that ArsRM is a difunctional protein with transcriptional regulation and methyltransferase activities. Expression of ArsRM in E. coli increased its arsenite resistance to 1.5 mM. The arsenite methylation activity of ArsRM and its ability to bind to its own gene promoter were confirmed. The As(III)-binding site (ABS) and S-adenosylmethionine-binding motif are responsible for the difunctional characteristic of ArsRM.ConclusionsWe conclude that ArsRM promotes arsenite methylation and is able to bind to its own promoter region to regulate transcription. This difunctional characteristic directly connects methionine and arsenic metabolism. Our findings contribute important new knowledge about microbial arsenic resistance and detoxification. Future work should further explore how ArsRM regulates the met operon and the ars cluster.

Identification of Key Genes Associated with Heat Stress in Rats by Weighted Gene Co-Expression Network Analysis.

Heat stress has been a big challenge for animal survival and health due to global warming. However, the molecular processes driving heat stress response were unclear. In this study, we exposed the control group rats (n = 5) at 22 °C and the other three heat stress groups (five rats in each group) at 42 °C lasting 30, 60, and 120 min, separately. We performed RNA sequencing in the adrenal glands and liver and detected the levels of hormones related to heat stress in the adrenal gland, liver, and blood tissues. Weighted gene co-expression network analysis (WGCNA) was also performed. Results showed that rectal temperature and adrenal corticosterone levels were significantly negatively related to genes in the black module, which was significantly enriched in thermogenesis and RNA metabolism. The genes in the green-yellow module were strongly positively associated with rectal temperature and dopamine, norepinephrine, epinephrine, and corticosterone levels in the adrenal glands and were enriched in transcriptional regulatory activities under stress. Finally, 17 and 13 key genes in the black and green-yellow modules were identified, respectively, and shared common patterns of changes. Methyltransferase 3 (Mettl3), poly(ADP-ribose) polymerase 2 (Parp2), and zinc finger protein 36-like 1 (Zfp36l1) occupied pivotal positions in the protein-protein interaction network and were involved in a number of heat stress-related processes. Therefore, Parp2, Mettl3, and Zfp36l1 could be considered candidate genes for heat stress regulation. Our findings shed new light on the molecular processes underpinning heat stress.

Identification of the promoter region regulating the transcription of the REV7 gene

REV7 is involved in various biological processes including DNA repair and mutagenesis, cell cycle regulation, gene transcription, and carcinogenesis. REV7 is highly expressed in adult testicular germ cells as well as several malignant tumors. REV7 expression levels are associated with prognosis in several human cancers, however, the mechanism of REV7 transcriptional regulation has not been elucidated. In this study, we characterized the promoter region of the REV7 gene. A luciferase reporter assay using the human germ cell tumor cell line NEC8 was utilized to examine the upstream genomic region of REV7 for transcriptional activity, and two transcriptional activation regions were identified. We determined a small genomic region important for transcriptional activation using site-directed mutagenesis; this region is shared by several putative binding motifs for transcription factors, including the cAMP-responsive element modulator (CREM), cAMP-response element binding protein (CREB), and B-lymphocyte-induced maturation protein-1 (BLIMP-1). Exogenous CREM and CREB expression had no effect on the transcriptional activity in NEC8 cells or the human embryonic kidney cell line HEK293T. In contrast, exogenous BLIMP-1 expression increased luciferase reporter activity in HEK293T cells but unexpectedly decreased activity in NEC8 cells. Chromatin immunoprecipitation analysis demonstrated that BLIMP-1 binds to the genomic region near the binding motif in the REV7 promoter. Additionally, BLIMP-1 overexpression promoted endogenous REV7 expression in HEK293T cells. These findings suggest that BLIMP-1 may be a putative transcriptional regulator of REV7 in mammalian cells.

Transcriptional Activation of a Pro-Inflammatory Response (NF-κB, AP-1, IL-1β) by the Vibrio cholerae Cytotoxin (VCC) Monomer through the MAPK Signaling Pathway in the THP-1 Human Macrophage Cell Line.

This study describes, to some extent, the VCC contribution as an early stimulation of the macrophage lineage. Regarding the onset of the innate immune response caused by infection, the β form of IL-1 is the most important interleukin involved in the onset of the inflammatory innate response. Activated macrophages treated in vitro with VCC induced the activation of the MAPK signaling pathway in a one-hour period, with the activation of transcriptional regulators for a surviving and pro-inflammatory response, suggesting an explanation inspired and supported by the inflammasome physiology. The mechanism of IL-1β production induced by VCC has been gracefully outlined in murine models, using bacterial knockdown mutants and purified molecules; nevertheless, the knowledge of this mechanism in the human immune system is still under study. This work shows the soluble form of 65 kDa of the Vibrio cholerae cytotoxin (also known as hemolysin), as it is secreted by the bacteria, inducing the production of IL-1β in the human macrophage cell line THP-1. The mechanism involves triggering the early activation of the signaling pathway MAPKs pERK and p38, with the subsequent activation of (p50) NF-κB and AP-1 (cJun and cFos), determined by real-time quantitation. The evidence shown here supports that the monomeric soluble form of the VCC in the macrophage acts as a modulator of the innate immune response, which is consistent with the assembly of the NLRP3 inflammasome actively releasing IL-1β.

Abstract 1469: Visualization of endogenous EWSR1 in Ewing sarcoma cells reveals a regular nucleoplasmic organization that includes concentration at regions of active transcription

Abstract EWSR1, a member of the FET protein family, contains low complexity and nucleic acid binding domains and regulates transcription. Biochemical and depletion studies have demonstrated that EWSR1 regulates basal transcription, and that in Ewing sarcoma (EWS) cells expressing the fusion oncoprotein EWSR1::FLI1, EWSR1 may contribute to the deregulation of gene expression observed in this cancer. To further study EWSR1’s function in Ewing sarcoma, we generated reporter cell lines to visualize and quantify its endogenous expression within EWS cells. To generate EWSR1-fluorescent reporter A673 and TC-32 EWS cell lines, we used CRISPR-Cas9 and sgRNAs targeting the 5’ end of the first exon of EWSR1 and a donor plasmid consisting of the mNeonGreen (mNG) reporter gene, a G4S3 linker, and EWSR1 homology arm templates. Upon validation of successfully modified clones (A673 and TC-32), we used confocal microscopy to confirm EWSR1’s localization to the nucleoplasm. Also, consistent with previous analysis of EWSR1’s protein-protein interactions, we confirmed using immunoprecipitation that the mNG-EWSR1 protein retains its interaction with EWSR1::FLI1 and RNA polymerase II (RNA pol II) - total and phosphorylated (pS5 and pS2). FRAP analysis (Zeiss Airyscan) showed that in cells, EWSR1 exists in two fractions, one that rapidly exchanges (A673 T½: 9.47 secs; TC-32 T½: 6.13 secs) and one that remains bound for a longer duration (A673 T½: 92.15 secs; TC-32; T½: 52.63 secs). We next used structured illumination microscopy to interrogate EWSR1’s spatial organization in EWS cells at a high resolution (~100 nm). First, we determined that EWSR1’s organization within the nucleoplasm is regular as measured by a signal-to-signal distance of ~300 nm in both cell lines (A673 cells 297±6.71 nm; TC-32 cells 304±8.59 nm). Analysis of EWSR1’s spatial organization relative to nucleic acids and proteins that function in gene expression indicates that EWSR1 partially co-localizes with DNA (visualized using DAPI), Histone 3, BRD4 and MED1 (visualized using immunofluorescence - IF). In contrast, we observed EWSR1 colocalizes completely with nascent RNA (visualized using Click-IT RNA Alexa Fluor 488, Invitrogen) (Manders overlap coefficient (MOC) A673: 0.96±0.005; TC-32: 0.97±0.005). Furthermore, we detected over 90% colocalization of concentrated EWSR1 signals (defined by specific fluorescent intensities) with RNA pol II (IF) in states associated with transcriptional initiation (pS5) (MOC A673: 0.94±0.011; TC-32: 0.93±0.02) and elongation (pS2) (MOC A673: 0.95±0.02; TC-32: 0.97±0.06). These studies will aid analysis of changes in EWSR1’s localization within the nucleus and relative to proteins that regulate gene expression following inhibition of transcription, including the application of compounds that disrupt EWSR1::FLI1’s transcriptional activity. Citation Format: Soumya Sundara Rajan, Vernon Ebegboni, Tamara L. Jones, Patrick Pichling, Katelyn R. Ludwig, Raj Chari, Michael Kruhlak, Jadranka Loncarek, Natasha J. Caplen. Visualization of endogenous EWSR1 in Ewing sarcoma cells reveals a regular nucleoplasmic organization that includes concentration at regions of active transcription [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1469.

Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.

Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transposase accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods. We model this complex bias using a rule ensemble machine learning approach that integrates information from many input k-mers proximal to the ATAC sequence reads. We effectively characterize and correct single-nucleotide sequence biases and regional sequence biases of the Tn5 enzyme. Correction of enzymatic sequence bias is an important step in interpreting chromatin accessibility assays that aim to infer transcription factor binding and regulatory activity of elements in the genome.

Neurokinin-1 Receptor Antagonists as a Potential Novel Therapeutic Option for Osteosarcoma Patients.

Osteosarcoma is a bone tumor predominantly affecting children and adolescents with high malignant potential. It is a cause of serious public health challenges due to its high morbidity rates and metastatic potential. Metastasis in osteosarcoma may manifest either during treatment of the primary tumor, shortly after treatment, or a long time after the end of the treatment. So far, there are no therapeutics that can prevent or treat osteosarcoma metastasis. The peptide substance P (SP) and its high-affinity receptor, Neurokinin-1 (NK-1R), are known to positively correlate with osteosarcoma progression. Osteosarcoma cells overexpress NK-1R. SP is known to elicit the proliferation of osteosarcoma cells and induce angiogenesis and migration, leading to the invasion and metastasis of tumor cells. In contrast, NK-1R antagonists, such as aprepitant, inhibit the proliferation and induce the apoptosis of osteosarcoma cells. Aprepitant is also known to inhibit the migration of osteosarcoma cells, as well as reduce the expression levels and activities of transcriptional regulators of metastasis-related genes such as matrix metalloproteinases (MMP-2 and MMP-9), vascular endothelial growth factor (VEGF), and nuclear factor kappa B (NF-κB). These preceding studies highlighted the antimetastatic role of aprepitant in osteosarcoma Moreover, combination therapy consisting of chemotherapy and NK-1R antagonist increases the chemosensitization of osteosarcoma cells. Interestingly, this combination therapy in vitro and in vivo decreases the severe side-effects of chemotherapy and produces neuroprotection, hepatoprotection, nephroprotection, and cardioprotection. In this review, we provide an update on existing data and suggest the need to repurpose aprepitant for use as an antitumor drug for treatment of osteosarcoma, and they suggest the need for phase I and II clinical trials for assessment of its safety/efficacy.